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- PDB-5urw: Structure of the extended type VI secretion system sheath in Myxo... -

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Basic information

Entry
Database: PDB / ID: 5urw
TitleStructure of the extended type VI secretion system sheath in Myxococcus xanthus
Components
  • Hcp
  • TssB
  • TssC
KeywordsPROTEIN TRANSPORT / T6SS / type IV secretion / protein machine / secretion system / sheath / contractile
Function / homology
Function and homology information


Type VI secretion system TssC-like / TssC1, N-terminal / TssC1, C-terminal / EvpB/VC_A0108, tail sheath N-terminal domain / EvpB/VC_A0108, tail sheath gpW/gp25-like domain / Type VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp
Similarity search - Domain/homology
Uncharacterized protein / Type VI secretion protein / Type VI secretion system-associated protein
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 24 Å
AuthorsChang, Y.-W. / Rettberg, L.A. / Jensen, G.J.
CitationJournal: EMBO Rep / Year: 2017
Title: structures of an intact type VI secretion system revealed by electron cryotomography.
Authors: Yi-Wei Chang / Lee A Rettberg / Davi R Ortega / Grant J Jensen /
Abstract: The type VI secretion system (T6SS) is a versatile molecular weapon used by many bacteria against eukaryotic hosts or prokaryotic competitors. It consists of a cytoplasmic bacteriophage tail-like ...The type VI secretion system (T6SS) is a versatile molecular weapon used by many bacteria against eukaryotic hosts or prokaryotic competitors. It consists of a cytoplasmic bacteriophage tail-like structure anchored in the bacterial cell envelope via a cytoplasmic baseplate and a periplasmic membrane complex. Rapid contraction of the sheath in the bacteriophage tail-like structure propels an inner tube/spike complex through the target cell envelope to deliver effectors. While structures of purified contracted sheath and purified membrane complex have been solved, because sheaths contract upon cell lysis and purification, no structure is available for the extended sheath. Structural information about the baseplate is also lacking. Here, we use electron cryotomography to directly visualize intact T6SS structures inside cells. Using sub-tomogram averaging, we resolve the structure of the extended sheath and membrane-associated components including the baseplate. Moreover, we identify novel extracellular bacteriophage tail fiber-like antennae. These results provide new structural insights into how the extended sheath prevents premature disassembly and how this sophisticated machine may recognize targets.
History
DepositionFeb 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / em_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_software.name

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
1A: TssB
1B: TssC
1C: TssB
1D: TssC
1E: TssB
1F: TssC
1G: TssB
1H: TssC
1I: TssB
1J: TssC
1K: TssB
1L: TssC
11: Hcp
12: Hcp
13: Hcp
14: Hcp
15: Hcp
16: Hcp
2A: TssB
2B: TssC
2C: TssB
2D: TssC
2E: TssB
2F: TssC
2G: TssB
2H: TssC
2I: TssB
2J: TssC
2K: TssB
2L: TssC
21: Hcp
22: Hcp
23: Hcp
24: Hcp
25: Hcp
26: Hcp
3A: TssB
3B: TssC
3C: TssB
3D: TssC
3E: TssB
3F: TssC
3G: TssB
3H: TssC
3I: TssB
3J: TssC
3K: TssB
3L: TssC
31: Hcp
32: Hcp
33: Hcp
34: Hcp
35: Hcp
36: Hcp


Theoretical massNumber of molelcules
Total (without water)1,660,86654
Polymers1,660,86654
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
TssB


Mass: 18016.617 Da / Num. of mol.: 18 / Source method: isolated from a natural source
Source: (natural) Myxococcus xanthus (strain DK 1622) (bacteria)
Strain: DK 1622 / References: UniProt: Q1D305
#2: Protein
TssC


Mass: 56188.469 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus (bacteria) / Strain: DK 1622 / References: UniProt: Q1D304
#3: Protein
Hcp


Mass: 18065.271 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus (bacteria) / Strain: DK 1622 / References: UniProt: Q1D303

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Type VI secretion system / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Myxococcus xanthus DK 1622 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2UCSFTomoimage acquisition
4IMODCTF correction
11PEETfinal Euler assignment
12PEETclassification
13TOMO3D3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 24 Å / Resolution method: OTHER / Num. of particles: 687 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 29 / Num. of volumes extracted: 687

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